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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1033/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.36.0  (landing page)
Stefano de Pretis
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/INSPEcT
git_branch: RELEASE_3_20
git_last_commit: ce54116
git_last_commit_date: 2024-10-29 10:02:14 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for INSPEcT on kjohnson1

To the developers/maintainers of the INSPEcT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/INSPEcT.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: INSPEcT
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings INSPEcT_1.36.0.tar.gz
StartedAt: 2024-12-20 22:47:47 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 23:00:37 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 770.4 seconds
RetCode: 0
Status:   OK  
CheckDir: INSPEcT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings INSPEcT_1.36.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/INSPEcT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.36.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘INSPEcT’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
output_pars: no visible global function definition for ‘plot.new’
plotSingleRNADynamic: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot.new
Consider adding
  importFrom("graphics", "lines", "plot.new")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
makeSimDataset                  78.341  0.252  78.609
quantifyExpressionsFromBAMs     35.561  6.108  42.026
INSPEcT_diffsteady-class        31.295  0.217  31.515
rocCurve                        25.853  0.097  25.961
rocThresholds                   25.594  0.120  25.764
makeSimModel                    25.496  0.108  25.666
plotMA                          25.373  0.101  25.497
compareSteady                   23.966  0.105  24.089
quantifyExpressionsFromTrCounts 17.260  0.096  17.425
modelRates                      16.903  0.041  16.945
newINSPEcT                      14.674  0.046  14.724
processingDelay                 13.658  0.055  13.716
makeOscillatorySimModel          6.065  0.033   6.101
compareSteadyNoNascent           5.534  0.027   5.576
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.


Installation output

INSPEcT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL INSPEcT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘INSPEcT’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (INSPEcT)

Tests output


Example timings

INSPEcT.Rcheck/INSPEcT-Ex.timings

nameusersystemelapsed
AIC-INSPEcT-method0.2470.0080.256
Extract0.4350.0080.444
INSPEcT_diffsteady-class31.295 0.21731.515
calculateRatePvals0.2810.0040.285
chisqmodel0.2450.0050.250
chisqtest0.2460.0050.251
combine0.4160.0060.421
compareSteady23.966 0.10524.089
compareSteadyNoNascent5.5340.0275.576
convergence0.2460.0060.252
geneClass0.2840.0080.292
inHeatmap0.2850.0100.294
inspectFromPCR3.5810.0223.603
labeledSF0.2450.0060.251
logLik0.2470.0060.252
makeModelRates0.310.010.32
makeOscillatorySimModel6.0650.0336.101
makeSimDataset78.341 0.25278.609
makeSimModel25.496 0.10825.666
modelRates16.903 0.04116.945
modelRatesNF1.5240.0421.566
modelSelection0.2440.0040.248
modelingParams0.2440.0050.248
nGenes0.2450.0060.256
nTpts0.2440.0040.249
newINSPEcT14.674 0.04614.724
plotGene0.2920.0080.300
plotMA25.373 0.10125.497
processingDelay13.658 0.05513.716
quantifyExpressionsFromBAMs35.561 6.10842.026
quantifyExpressionsFromTrCounts17.260 0.09617.425
ratePvals0.2440.0090.253
ratesFirstGuess0.2440.0090.252
ratesFirstGuessVar0.2440.0080.253
removeModel0.3410.0080.349
rocCurve25.853 0.09725.961
rocThresholds25.594 0.12025.764
split0.3270.0050.332
tpts0.2440.0060.250
viewConfidenceIntervals0.2450.0090.254
viewModelRates0.2430.0080.252